ArticlePLoS neglected tropical diseases2012
Virus identification in unknown tropical febrile illness cases using deep sequencing.
Article in PLoS neglected tropical diseases, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
85 citing papers in PubMed, 1 synthesis or guideline pooled it, 171 citations in OpenAlex.
- Systematic review and meta-analysis of virome profiles and quantification of Torque teno virus load in blood of acute febrile illness patients.Scientific reports · 2025Pooled it
- Metagenomic next-generation sequencing in the diagnosis of viral encephalitis.World journal of virology · 2026Review
- Identifying viral infections through metagenomic Next Generation Sequencing of undiagnosed respiratory fevers in Madagascar (2014-2019).BMC infectious diseases · 2026Article
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
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- Accelerating Cleavage Activity of CRISPR-Cas13 System on a Microfluidic Chip for Rapid Detection of RNA.Analytical chemistry · 2025Article
- Species-specific RNA barcoding technology for rapid and accurate identification of four types of influenza virus.BMC genomics · 2025Article
- Diverse Facets of Nonhuman Sequences in Read Outputs of the Human Next-Generation Sequencing Data and Their Relevance with Viruses.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Nucleic acid degradation after long-term dried blood spot storage.Molecular ecology resources · 2024Article
- Article
- Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics.Diagnostics (Basel, Switzerland) · 2023Review
- Clinical Evaluation of Metagenomic Next-Generation Sequencing and Identification of Risk Factors in Patients with Severe Community-Acquired Pneumonia.Infection and drug resistance · 2023Article
- A metagenomic insight into the Yangtze finless porpoise virome.Frontiers in veterinary science · 2022Article
- Recent Improvements in CRISPR-Based Amplification-Free Pathogen Detection.Frontiers in microbiology · 2021Review
- The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection.Frontiers in cellular and infection microbiology · 2021Review
- IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.GigaScience · 2020Article
- Review
- Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses.Journal of virological methods · 2020Article
- DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing.Microbial genomics · 2020Article
- Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus.PloS one · 2020Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
Dengue virus is an emerging infectious agent that infects an estimated 50-100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.